add warning message for the deprecated methods

[melodyyzh]

Description

Added deprecation warnings for the following methods:

• _InternalCustomUpdater.update.
• _InternalCustomTuner.tune.
• _InternalCustomWriter.write.
• HDF5Log.write.

Motivation and context

Resolves #1648

How has this been tested?

Used the existing python tests

Change log

Deprecated:

* ``_InternalCustomUpdater.update``.
  (`#1692 <https://github.com/glotzerlab/hoomd-blue/pull/1692>`__).
* ``_InternalCustomTuner.tune``.
  (`#1692 <https://github.com/glotzerlab/hoomd-blue/pull/1692>`__).  
* ``_InternalCustomWriter.write``.
  (`#1692 <https://github.com/glotzerlab/hoomd-blue/pull/1692>`__).
* ``HDF5Log.write``.
  (`#1692 <https://github.com/glotzerlab/hoomd-blue/pull/1692>`__).

Checklist:

• I have reviewed the Contributor Guidelines.
• I agree with the terms of the HOOMD-blue Contributor Agreement.
• My name is on the list of contributors (sphinx-doc/credits.rst) in the pull request source branch.

[joaander]

Thanks! I have some suggestions to fix the grammar which I will apply and then merge.